There's really no good reason this drive isn't being detected. It's probably a safety feature of the computer since booting off CD or USB is an easy way to get to the files in the HDD. Look through the BIOS settings as already recommended.

It may also be possible that your booted OS doesn't understand the file system of the HDD OS. This would only be a problem if they're different operating systems. If it can't understand the file system, it probably wouldn't attempt to mount it since you can do permanent damage mounting a drive with an incompatible file system.

I have a new HDD, On which the operating System in USB should be copied.Since the Operating System in USB is Linux, It is possible to copy the entire file system from one booteable media to another, I have tried this with two HDD's and made it work.

But when i try to copy file system from USB to HDD, I can't able to detect HDD on boot and manually.

Typically you can manually mount a hard drive if you can find it. Off the top of my head, I can't remember how you go about mounting a hard drive to a logical drive (look up the mount command, also, Linux has a fairly straight forward drive naming convention so you may be able to easily mount it).